This invention relates to scanning a surface and more particularly to such a system which can achieve constant scan length per data sample.
Scanning imaging systems form a map of some characteristic of a surface of interest by exposing the surface to light and measuring a response from the surface. A focused beam of light is moved in a deliberate and repeatable pattern with respect to the surface. The response is generally time-correlated to the position of the scanning beam in order to form a final map of the property with respect to a location on the surface. In most situations, it is important to be able to infer the position of the surface represented by each pixel and to be able to guarantee that the pixel spacing is uniform within some tolerance dictated by the size of the features being scanned.
Relative motion between the light beam and the surface can be achieved by maintaining the surface stationary and moving the beam or, alternatively, keeping the beam stationary while moving the surface. A high performance (high numerical aperture) optical system of reasonable cost, often has a scanner in which a surface moves while the illuminating beam stays in a constant position relative to the beam optics. Such an arrangement results in the desirable property of high numerical aperture. Alternatively, the surface may remain fixed with the light beam being moved. The components that position the surface relative to the beam generally exhibit some systematic position errors that are a function of position or time. These errors degrade the quality of the final map of the desired property with respect to a location on the surface.
The present invention has particular application to gene chips which contain arrays of short DNA chains in an array of sequences bound to a substrate (usually glass). The chip is indexed so that the particular DNA sequence bound in any area is known. A region having a homogeneous composition is referred to as a xe2x80x9cfeature.xe2x80x9d The DNA chips can be incubated with a solution containing RNA or DNA bound to a fluorescent tag, allowing the binding of RNA to individual features. Such systems can be used for the determination of both genotype and gene expression levels.
If fluorescence is observed in a particular region, binding has occurred and a DNA sequence is identified by consulting the index of DNA positions on the chip. The present invention is particularly useful in this context. As will be discussed below, the present invention sets forth a methodology for measuring and compensating position errors which may be a function of position or time to an arbitrary level of linearity.
In one aspect, the apparatus for scanning a surface includes an optical system to generate a light beam and to deliver the beam to a surface. A carrier supports the surface and is mounted for reciprocating motion with respect to the light beam to form one axis of a raster. Of course, the surface may be fixed with the optics arranged to sweep the light beam. A propulsion system generates forces for moving the carrier and a position sensor generates an output signal representing the surface position with respect to the light beam. A servo system responsive to the output signal is provided for commanding the propulsion system to move the carrier at a substantially constant speed in a scanning region. A control system responsive to the output signal is provided to modulate a sample period reciprocally to carrier speed to achieve substantially constant scan length per sample and to control data acquisition timing.
In one embodiment, the position sensor, which is monotonic and repeatable, is selected from a group including a counting position encoder, optical encoder, magnetic encoder, capacitive encoder, laser interferometer, an LVDT or reflected optical triangulation device. The propulsion system may include a motor, voice coil, a galvanometer, a gas jet or a graphite piston in a glass cylinder powered by a gas or liquid. A state observer may be provided to generate an estimate of carrier speed for use by the sample period modulation system. A system may also be provided for compensating for variable integral illumination per sample. One such technique includes scaling the amplitude of a measured signal by a function of a ratio of an actual sample period to a nominal sample period.
In yet another embodiment of the invention, data acquisition timing is controlled by a state machine that triggers data acquisition when a selected number of new counts in a correct direction has occurred. The inputs to the state machine may be quadrature decoded direction and quadrature decoded count information. The state machine is programmed so that new counts in the correct direction are detected by counting backwards quadrature state changes and incrementing a trigger counter on quadrature state changes only when a backwards counter is zero.
In yet another embodiment, data acquisition timing is triggered by the first equivalence of an actual position value and a selected trigger position in which a counter is rapidly incremented, for example, ten times.
The approach of the present invention permits a highly linear scan (in the sense that the servo system actively regulates the sample period to give constant pixel size) even in the presence of disturbances such as friction and vibration.